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.\" ========================================================================
.\"
.IX Title "ALTREE-CONVERT 1p"
.TH ALTREE-CONVERT 1p "2020-11-09" "perl v5.32.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
altree\-convert \- Title...
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
altree-convert [options]
.PP
.Vb 10
\& Options:
\&    \-\-version             program version
\&    \-\-short\-help|h        brief help message
\&    \-\-help                help message with options descriptions
\&    \-\-man                 full documentation
\&    \-\-first\-input\-file|i  input file 1
\&    \-\-second\-input\-file|j input file 2 (not mandatory)
\&    \-\-output\-file|o       output file
\&    \-\-case\-control\-output|c  output containing the nb cases/controls
\&    \-\-data\-type|t         DNA|NUM
\&    \-\-phylo\-prog|p        PAUP|PHYLIP
\&    \-\-reconstruct\-prog|r  PHASE|FAMHAP
\&    \-\-data\-quali|q        Type of data: qualitative or quantitative
\&    \-\-nbind\-threshold|s   Minimum number of individuals ecquired to keep an haplotype
.Ve
.SH "OPTIONS"
.IX Header "OPTIONS"
.IP "\fB\-\-version\fR" 8
.IX Item "--version"
Print the program version and exits.
.IP "\fB\-\-short\-help\fR" 8
.IX Item "--short-help"
Print a brief help message and exits.
.IP "\fB\-\-help\fR" 8
.IX Item "--help"
Print a help message with options descriptions and exits.
.IP "\fB\-\-man\fR" 8
.IX Item "--man"
Prints the manual page and exits.
.IP "\fB\-\-first\-input\-file|i\fR" 8
.IX Item "--first-input-file|i"
Input file 1 (output of the haplotype reconstruction program)
.IP "\fB\-\-second\-input\-file|j\fR" 8
.IX Item "--second-input-file|j"
Input file 2 (second output of famhap or file containig the disease status)
.IP "\fB\-\-output\-file|o\fR" 8
.IX Item "--output-file|o"
Output file
.IP "\fB\-\-case\-control\-output|c\fR" 8
.IX Item "--case-control-output|c"
Output file containing the number of cases and controls carrying each haplotype
.ie n .IP "\fB\-\-data\-type|t\fR ""DNA""|""SNP""" 8
.el .IP "\fB\-\-data\-type|t\fR \f(CWDNA\fR|\f(CWSNP\fR" 8
.IX Item "--data-type|t DNA|SNP"
Type of data: \s-1DNA\s0 (\s-1ATGCU\s0) or \s-1SNP\s0 (0\-1)
.ie n .IP "\fB\-\-phylo\-prog|p\fR ""phylip""|""paup""" 8
.el .IP "\fB\-\-phylo\-prog|p\fR \f(CWphylip\fR|\f(CWpaup\fR" 8
.IX Item "--phylo-prog|p phylip|paup"
Phylogeny reconstruction program
.ie n .IP "\fBreconstruct\-prog|r\fR ""famhap|phase""" 8
.el .IP "\fBreconstruct\-prog|r\fR \f(CWfamhap|phase\fR" 8
.IX Item "reconstruct-prog|r famhap|phase"
Haplotype reconstruction program
.ie n .IP "\fBdata\-quali|q\fR ""qualitative|quantitative""" 8
.el .IP "\fBdata\-quali|q\fR \f(CWqualitative|quantitative\fR" 8
.IX Item "data-quali|q qualitative|quantitative"
Type of data analyzed
.IP "\fBnbind\-threshold|s\fR" 8
.IX Item "nbind-threshold|s"
Minimal number of individuals carrying an haplotype recquired to keep it for further analysis. If you want to keep all haplotypes, you must affect 0 to this variable
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fBThis program\fR will read the given input file(s) and  generate an input file for the phylogenetic reconstruction software paup or phylip/paml